[med-svn] [cwltool] 01/01: Imported Upstream version 1.0.20160209222805

[Michael Crusoe]

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misterc-guest pushed a commit to annotated tag upstream/1.0.20160209222805
in repository cwltool.

commit c36e784ce19d6eed2192e2bc69d3e807f0b3fb93
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Mon Feb 22 10:04:24 2016 -0800

    Imported Upstream version 1.0.20160209222805
---
 PKG-INFO                  |  2 +-
 cwltool.egg-info/PKG-INFO |  2 +-
 cwltool/main.py           | 41 +++++++++++++++++++++++++++++++++++++++++
 setup.cfg                 |  2 +-
 4 files changed, 44 insertions(+), 3 deletions(-)

diff --git a/PKG-INFO b/PKG-INFO
index aaeefe9..cdf478d 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: cwltool
-Version: 1.0.20160203221531
+Version: 1.0.20160209222805
 Summary: Common workflow language reference implementation
 Home-page: https://github.com/common-workflow-language/common-workflow-language
 Author: Common workflow language working group
diff --git a/cwltool.egg-info/PKG-INFO b/cwltool.egg-info/PKG-INFO
index aaeefe9..cdf478d 100644
--- a/cwltool.egg-info/PKG-INFO
+++ b/cwltool.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: cwltool
-Version: 1.0.20160203221531
+Version: 1.0.20160209222805
 Summary: Common workflow language reference implementation
 Home-page: https://github.com/common-workflow-language/common-workflow-language
 Author: Common workflow language working group
diff --git a/cwltool/main.py b/cwltool/main.py
index 72d3a45..832002b 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -99,6 +99,7 @@ def arg_parser():
                         help="Print corresponding RDF graph for workflow and exit")
     exgroup.add_argument("--print-dot", action="store_true", help="Print workflow visualization in graphviz format and exit")
     exgroup.add_argument("--print-pre", action="store_true", help="Print CWL document after preprocessing.")
+    exgroup.add_argument("--print-deps", action="store_true", help="Print CWL document dependencies from $import, $include, $schemas")
     exgroup.add_argument("--version", action="store_true", help="Print version and exit")
     exgroup.add_argument("--update", action="store_true", help="Update to latest CWL version, print and exit")
 
@@ -412,6 +413,42 @@ def load_job_order(args, t, parser):
     return (job_order_object, input_basedir)
 
 
+def scandeps(base, doc):
+    r = []
+    if isinstance(doc, dict):
+        if "$import" in doc:
+            p = os.path.join(base, doc["$import"])
+            with open(p) as f:
+                r.append({
+                    "class": "File",
+                    "path": p,
+                    "secondaryFiles": scandeps(os.path.dirname(p), yaml.load(f))
+                })
+        elif "$include" in doc:
+            p = os.path.join(base, doc["$include"])
+            r.append({
+                "class": "File",
+                "path": p
+            })
+        elif "$schemas" in doc:
+            for s in doc["$schemas"]:
+                p = os.path.join(base, s)
+                r.append({
+                    "class": "File",
+                    "path": p
+                })
+        else:
+            for d in doc.itervalues():
+                r.extend(scandeps(base, d))
+    elif isinstance(doc, list):
+        for d in doc:
+            r.extend(scandeps(base, d))
+    return r
+
+def print_deps(fn):
+    with open(fn) as f:
+        print json.dumps(scandeps(os.path.dirname(fn), yaml.load(f)), indent=4)
+
 def main(args=None,
          executor=single_job_executor,
          makeTool=workflow.defaultMakeTool,
@@ -451,6 +488,10 @@ def main(args=None,
         _logger.error("CWL document required")
         return 1
 
+    if args.print_deps:
+        print_deps(args.workflow)
+        return 0
+
     try:
         t = load_tool(args.workflow, args.update, args.strict, makeTool, args.debug,
                       print_pre=args.print_pre,
diff --git a/setup.cfg b/setup.cfg
index 9d8b109..c70c7be 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
 [egg_info]
-tag_build = .20160203221531
+tag_build = .20160209222805
 tag_date = 0
 tag_svn_revision = 0
 

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